Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X

A

acorr() (in module pytraj), [1]
(in module pytraj.all_actions)
ActionDict (class in pytraj)
ActionList (class in pytraj)
(class in pytraj.c_action.actionlist)
add() (pytraj.ActionList method)
(pytraj.c_action.actionlist.ActionList method)
add_angles (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
add_atom() (pytraj.AtomMask method)
(pytraj.Topology method)
(pytraj.core.c_core.AtomMask method)
(pytraj.topology.Topology method)
add_atom_range() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
add_atoms() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
add_bonds (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
add_dihedrals (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
add_selected_indices() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
align_principal_axis() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.trajectory.Trajectory method)
AnalysisDict (class in pytraj)
angle() (in module pytraj), [1]
(in module pytraj.all_actions)
angle_indices (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
angles (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
append() (pytraj.Trajectory method)
(pytraj.trajectory.Trajectory method)
append_xyz() (pytraj.Frame method)
(pytraj.Trajectory method)
(pytraj.frame.Frame method)
(pytraj.trajectory.Trajectory method)
ArgList (class in pytraj.core.c_core)
as_2darray() (in module pytraj.tools)
as_3darray() (in module pytraj.tools)
at() (pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
Atom (class in pytraj)
atom() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
atom_indices() (pytraj.Topology method)
(pytraj.topology.Topology method)
atom_names (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
atomic_number (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)
atomiccorr() (in module pytraj)
(in module pytraj.all_actions)
atomicfluct() (in module pytraj)
(in module pytraj.all_actions)
atomlist (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
AtomMask (class in pytraj)
(class in pytraj.core.c_core)
atoms (pytraj.Topology attribute)
(pytraj.topology.SimplifiedTopology attribute)
(pytraj.topology.Topology attribute)
autoimage() (in module pytraj), [1], [2]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)

B

begin_atom (pytraj.Molecule attribute)
bfactors() (in module pytraj), [1]
(in module pytraj.all_actions)
block_average() (in module pytraj.tools)
bond_indices (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
bonded_indices() (pytraj.Atom method)
bonds (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
box (pytraj.Frame attribute)
(pytraj.Topology attribute)
(pytraj.frame.Frame attribute)
(pytraj.topology.Topology attribute)
box() (in module pytraj.vector), [1]
boxcenter() (in module pytraj.vector), [1]

C

calc_alpha() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_beta() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_chin() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_chip() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_delta() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_dssp() (in module pytraj.dssp_analysis)
calc_epsilon() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_gamma() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_ired_vector_and_matrix() (in module pytraj.nmr)
calc_multidihedral() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_NH_order_parameters() (in module pytraj.nmr)
calc_nu1() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_nu2() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_omega() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_phi() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_psi() (in module pytraj)
(in module pytraj.dihedral_analysis)
calc_vector() (in module pytraj)
calc_zeta() (in module pytraj)
(in module pytraj.dihedral_analysis)
center() (in module pytraj), [1]
(in module pytraj.all_actions)
(in module pytraj.vector), [1]
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
center_of_geometry() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.frame.Frame method)
center_of_mass() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.frame.Frame method)
chain (pytraj.Atom attribute)
charge (pytraj.Atom attribute)
(pytraj.Topology attribute)
(pytraj.topology.SimplifiedAtom attribute)
(pytraj.topology.Topology attribute)
check_structure() (in module pytraj)
(in module pytraj.all_actions)
closest() (in module pytraj), [1]
(in module pytraj.all_actions)
Command (class in pytraj.core.c_core)
command_is() (pytraj.core.c_core.ArgList method)
compose() (in module pytraj.tools)
compute() (in module pytraj.c_action.actionlist)
(pytraj.ActionList method)
(pytraj.CpptrajState method)
(pytraj.c_action.actionlist.ActionList method)
(pytraj.core.c_core.CpptrajState method)
concat_dict() (in module pytraj.tools)
coordinates (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
copy() (pytraj.Atom method)
(pytraj.Frame method)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.core.c_core.NameType method)
(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
correl() (in module pytraj.matrix), [1]
corrplane() (in module pytraj.vector), [1]
count() (pytraj.topology.SimplifiedAtom method)
(pytraj.topology.SimplifiedResidue method)
(pytraj.topology.SimplifiedTopology method)
covar() (in module pytraj.matrix), [1]
CpptrajState (class in pytraj)
(class in pytraj.core.c_core)
crank() (in module pytraj)

D

data (pytraj.ActionList attribute)
(pytraj.CpptrajState attribute)
(pytraj.c_action.actionlist.ActionList attribute)
(pytraj.core.c_core.CpptrajState attribute)
(pytraj.hbond_analysis.DatasetHBond attribute), [1]
datafilelist (pytraj.core.c_core.CpptrajState attribute)
(pytraj.CpptrajState attribute)
DatasetHBond (class in pytraj.hbond_analysis), [1]
datasetlist (pytraj.core.c_core.CpptrajState attribute)
(pytraj.CpptrajState attribute)
diagonalize() (in module pytraj.matrix), [1]
dict_to_ndarray() (in module pytraj.tools)
diffusion() (in module pytraj)
(in module pytraj.all_actions)
dihcovar() (in module pytraj.matrix), [1]
dihedral() (in module pytraj), [1]
(in module pytraj.all_actions)
dihedral_indices (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
dihedrals (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
dipole() (in module pytraj.vector), [1]
dir_() (in module pytraj.tools)
dispatch() (in module pytraj)
(pytraj.core.c_core.Command method)
dist() (in module pytraj.matrix), [1]
distance() (in module pytraj), [1]
(in module pytraj.all_actions)
distance_rmsd() (in module pytraj)
(in module pytraj.all_actions)
distcovar() (in module pytraj.matrix), [1]
donor_acceptor (pytraj.hbond_analysis.DatasetHBond attribute), [1]
dssp() (in module pytraj)
dssp_allatoms() (in module pytraj.dssp_analysis)
dssp_allresidues() (in module pytraj.dssp_analysis)

E

element (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)
end_atom (pytraj.Molecule attribute)
esander() (in module pytraj)
(in module pytraj.energy_analysis)
estimate_size() (in module pytraj.tools)

F

filelist (pytraj.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
FileName (class in pytraj.core.c_core)
filename (pytraj.Topology attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.topology.Topology attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
filename() (pytraj.topology.ParmFile method)
find_lib() (in module pytraj.tools)
first (pytraj.Residue attribute)
(pytraj.topology.SimplifiedResidue attribute)
first_atom_index (pytraj.Residue attribute)
flatten() (in module pytraj.tools)
force (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
Frame (class in pytraj)
(class in pytraj.frame)
FrameIterator (class in pytraj.frameiter)
from_dict() (pytraj.Topology method)
(pytraj.topology.Topology method)
from_iterable() (pytraj.Trajectory class method)
(pytraj.trajectory.Trajectory class method)
fullname (pytraj.core.c_core.FileName attribute)

G

gb_radius (pytraj.Atom attribute)
get_amber_mask() (pytraj.hbond_analysis.DatasetHBond method), [1]
get_average_frame() (in module pytraj)
(in module pytraj.all_actions)
get_key_double() (pytraj.core.c_core.ArgList method)
get_key_int() (pytraj.core.c_core.ArgList method)
get_next_double() (pytraj.core.c_core.ArgList method)
get_next_integer() (pytraj.core.c_core.ArgList method)
get_next_mask() (pytraj.core.c_core.ArgList method)
get_next_string() (pytraj.core.c_core.ArgList method)
get_next_tag() (pytraj.core.c_core.ArgList method)
get_state() (pytraj.core.c_core.Command method)
get_state_from_string() (pytraj.core.c_core.Command method)
get_string_key() (pytraj.core.c_core.ArgList method)
get_velocity() (in module pytraj)
(in module pytraj.all_actions)
grep_key() (in module pytraj.tools)
grid() (in module pytraj)
(in module pytraj.all_actions)
groupby() (in module pytraj.tools)

H

has_box() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
has_force() (pytraj.Frame method)
(pytraj.frame.Frame method)
has_key() (pytraj.core.c_core.ArgList method)
has_velocity() (pytraj.Frame method)
(pytraj.frame.Frame method)
hbond() (in module pytraj.hbond_analysis), [1]

I

idea() (in module pytraj.matrix), [1]
index (pytraj.Atom attribute)
(pytraj.Residue attribute)
(pytraj.topology.SimplifiedAtom attribute)
(pytraj.topology.SimplifiedResidue attribute)
index() (pytraj.topology.SimplifiedTopology method)
indices (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
indices_bonded_to() (pytraj.Topology method)
(pytraj.topology.Topology method)
invert_mask() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
ired_vector_and_matrix() (in module pytraj.nmr)
is_() (pytraj.Frame method)
(pytraj.frame.Frame method)
is_bonded_to() (pytraj.Atom method)
is_empty() (pytraj.AtomMask method)
(pytraj.Topology method)
(pytraj.core.c_core.ArgList method)
(pytraj.core.c_core.AtomMask method)
(pytraj.topology.Topology method)
is_setup (pytraj.ActionList attribute)
(pytraj.c_action.actionlist.ActionList attribute)
is_solvent() (pytraj.Molecule method)
(pytraj.Residue method)
iterchunk() (in module pytraj)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
iterframe() (in module pytraj)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
iteritems() (in module pytraj.tools)
iterload() (in module pytraj)
(in module pytraj.io)
iterload_remd() (in module pytraj)
(in module pytraj.io)

J

jcoupling() (in module pytraj), [1]
(in module pytraj.all_actions)
join() (pytraj.Topology method)
(pytraj.topology.Topology method)

K

keys() (pytraj.ActionDict method)
(pytraj.AnalysisDict method)
kmeans() (in module pytraj.cluster), [1]

L

last (pytraj.Residue attribute)
(pytraj.topology.SimplifiedResidue attribute)
last_atom_index (pytraj.Residue attribute)
load() (in module pytraj)
(in module pytraj.io)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
load_cpptraj_file() (in module pytraj)
(in module pytraj.io)
load_ParmEd() (in module pytraj)
(in module pytraj.io)
load_pdb_rcsb() (in module pytraj)
(in module pytraj.io)
load_remd() (in module pytraj)
(in module pytraj.io)
load_sample_data() (in module pytraj)
(in module pytraj.io)
load_topology() (in module pytraj)
(in module pytraj.io)
lowestcurve() (in module pytraj)
(in module pytraj.all_actions)

M

make_fake_topology() (in module pytraj.tools)
make_structure() (in module pytraj)
(in module pytraj.all_actions)
mask_expression() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
mask_string (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
mass (pytraj.Atom attribute)
(pytraj.Frame attribute)
(pytraj.Topology attribute)
(pytraj.frame.Frame attribute)
(pytraj.topology.SimplifiedAtom attribute)
(pytraj.topology.Topology attribute)
match() (pytraj.core.c_core.NameType method)
mean_and_error() (in module pytraj.tools)
mean_structure() (in module pytraj)
(in module pytraj.all_actions)
merge_coordinates() (in module pytraj.tools)
merge_frame_from_trajs() (in module pytraj.tools)
merge_frames() (in module pytraj.tools)
merge_trajs() (in module pytraj.tools)
metadata (pytraj.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
mindist() (in module pytraj), [1]
(in module pytraj.all_actions)
minimage() (in module pytraj.vector), [1]
Molecule (class in pytraj)
moleculelist (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
molnum (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)
mols (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
molsurf() (in module pytraj), [1]
(in module pytraj.all_actions)
moving_average() (in module pytraj.tools)
multidihedral() (in module pytraj), [1]
(in module pytraj.all_actions)
multivector() (in module pytraj)
(in module pytraj.all_actions)
mwcovar() (in module pytraj.matrix), [1]

N

n_args (pytraj.core.c_core.ArgList attribute)
n_atoms (pytraj.AtomMask attribute)
(pytraj.Frame attribute)
(pytraj.Molecule attribute)
(pytraj.Residue attribute)
(pytraj.Topology attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.core.c_core.AtomMask attribute)
(pytraj.frame.Frame attribute)
(pytraj.frameiter.FrameIterator attribute)
(pytraj.topology.Topology attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
n_bonds (pytraj.Atom attribute)
n_frames (pytraj.ActionList attribute)
(pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.c_action.actionlist.ActionList attribute)
(pytraj.frame.Frame attribute)
(pytraj.frameiter.FrameIterator attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
n_grams() (in module pytraj.tools)
n_mols (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
n_residues (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
n_selected (pytraj.AtomMask attribute)
(pytraj.core.c_core.AtomMask attribute)
n_solvents (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
name (pytraj.Atom attribute)
(pytraj.Residue attribute)
(pytraj.topology.SimplifiedAtom attribute)
(pytraj.topology.SimplifiedResidue attribute)
NameType (class in pytraj.core.c_core)
nastruct() (in module pytraj), [1]
native_contacts() (in module pytraj)
(in module pytraj.all_actions)
NH_order_parameters() (in module pytraj.nmr)
ntype() (pytraj.Residue method)

O

original_resid (pytraj.Residue attribute)

P

pairdist() (in module pytraj)
(in module pytraj.all_actions)
pairwise_distance() (in module pytraj)
(in module pytraj.all_actions)
pairwise_rmsd() (in module pytraj), [1]
(in module pytraj.all_actions)
ParmFile (class in pytraj.topology)
pca() (in module pytraj)
(in module pytraj.all_actions)
pipe() (in module pytraj.c_action.actionlist)
pmap_mpi() (in module pytraj.parallel.mpi)
post_process() (pytraj.ActionList method)
(pytraj.c_action.actionlist.ActionList method)
principal() (in module pytraj.vector), [1]
(pytraj.TrajectoryIterator method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
principal_axes() (in module pytraj), [1]
(in module pytraj.all_actions)
projection() (in module pytraj)
(in module pytraj.all_actions)
pucker() (in module pytraj)
(in module pytraj.all_actions)
pytraj (module)
pytraj.all_actions (module)
pytraj.c_action.actionlist (module)
pytraj.cluster (module)
pytraj.core.c_core (module)
pytraj.dihedral_analysis (module)
pytraj.dssp_analysis (module)
pytraj.energy_analysis (module)
pytraj.frame (module)
pytraj.frameiter (module)
pytraj.hbond_analysis (module), [1]
pytraj.io (module)
pytraj.matrix (module), [1]
pytraj.nmr (module)
pytraj.parallel.mpi (module)
pytraj.tools (module)
pytraj.topology (module)
pytraj.trajectory (module)
pytraj.trajectory_iterator (module)
pytraj.vector (module), [1]

R

radgyr() (in module pytraj), [1]
(in module pytraj.all_actions)
randomize_ions() (in module pytraj), [1]
(in module pytraj.all_actions)
rdf() (in module pytraj)
(in module pytraj.all_actions)
read_gaussian_output() (in module pytraj.tools)
read_json() (in module pytraj)
(in module pytraj.io)
read_pickle() (in module pytraj)
(in module pytraj.io)
read_to_array() (in module pytraj.tools)
readparm() (pytraj.topology.ParmFile method)
replace_asterisk() (pytraj.core.c_core.NameType method)
replicate_cell() (in module pytraj), [1]
(in module pytraj.all_actions)
resid (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)
Residue (class in pytraj)
residue() (pytraj.Topology method)
(pytraj.topology.Topology method)
residue_names (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
residuelist (pytraj.Topology attribute)
(pytraj.topology.Topology attribute)
residues (pytraj.Topology attribute)
(pytraj.topology.SimplifiedTopology attribute)
(pytraj.topology.Topology attribute)
resname (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)
reverse() (pytraj.Trajectory method)
(pytraj.trajectory.Trajectory method)
rmsd() (in module pytraj), [1], [2]
(in module pytraj.all_actions)
(in module pytraj.tools)
(pytraj.Frame method)
(pytraj.frame.Frame method)
rmsd_1darray() (in module pytraj.tools)
rmsd_nofit() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.frame.Frame method)
rmsd_perres() (in module pytraj), [1]
(in module pytraj.all_actions)
rmsfit() (pytraj.Frame method)
(pytraj.Trajectory method)
(pytraj.frame.Frame method)
(pytraj.trajectory.Trajectory method)
rotate() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
rotate_dihedral() (in module pytraj)
rotation_matrix() (in module pytraj)
(in module pytraj.all_actions)
run() (pytraj.core.c_core.CpptrajState method)
(pytraj.CpptrajState method)

S

save() (in module pytraj)
(in module pytraj.io)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.frameiter.FrameIterator method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
scale() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
search_hbonds() (in module pytraj)
search_neighbors() (in module pytraj), [1]
(in module pytraj.all_actions)
select() (in module pytraj)
(pytraj.Topology method)
(pytraj.topology.Topology method)
selected_indices() (pytraj.AtomMask method)
(pytraj.core.c_core.AtomMask method)
set_cpptraj_verbose() (in module pytraj)
set_dihedral() (in module pytraj)
(in module pytraj.all_actions)
set_distance_mask_reference() (pytraj.Topology method)
(pytraj.topology.Topology method)
set_first() (pytraj.Molecule method)
set_integer_mask() (pytraj.Topology method)
(pytraj.topology.Topology method)
set_last() (pytraj.Molecule method)
set_last_atom() (pytraj.Residue method)
set_mass() (pytraj.Frame method)
(pytraj.frame.Frame method)
set_mol() (pytraj.Atom method)
set_no_solvent() (pytraj.Molecule method)
set_nobox() (pytraj.Frame method)
(pytraj.Topology method)
(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
set_solvent() (pytraj.Molecule method)
(pytraj.Topology method)
(pytraj.topology.Topology method)
setup() (pytraj.ActionList method)
(pytraj.c_action.actionlist.ActionList method)
shape (pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.frame.Frame attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
show_versions() (in module pytraj)
SimplifiedAtom (class in pytraj.topology)
SimplifiedResidue (class in pytraj.topology)
SimplifiedTopology (class in pytraj.topology)
simplify() (pytraj.Topology method)
(pytraj.topology.Topology method)
size (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
split() (in module pytraj.tools)
split_and_write_traj() (in module pytraj.tools)
split_traj_by_residues() (in module pytraj.tools)
start_new_mol() (pytraj.Topology method)
(pytraj.topology.Topology method)
strip() (in module pytraj)
(in module pytraj.all_actions)
(pytraj.Frame method)
(pytraj.Topology method)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.frame.Frame method)
(pytraj.topology.Topology method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
summary() (pytraj.Topology method)
(pytraj.topology.Topology method)
superpose() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
surf() (in module pytraj)
(in module pytraj.all_actions)
swap_atoms (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)

T

temperature (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
temperatures (pytraj.trajectory_iterator.TrajectoryIterator attribute)
(pytraj.TrajectoryIterator attribute)
time (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
timecorr() (in module pytraj), [1]
(in module pytraj.all_actions)
to_buffer() (pytraj.core.c_core.NameType method)
to_dataframe() (pytraj.Topology method)
(pytraj.topology.Topology method)
to_dict() (pytraj.hbond_analysis.DatasetHBond method), [1]
(pytraj.Topology method)
(pytraj.topology.Topology method)
to_json() (in module pytraj)
(in module pytraj.io)
to_ndarray() (pytraj.Frame method)
(pytraj.frame.Frame method)
to_parmed() (pytraj.Topology method)
(pytraj.topology.Topology method)
to_pickle() (in module pytraj)
(in module pytraj.io)
top (pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.frame.Frame attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
Topology (class in pytraj)
(class in pytraj.topology)
topology (pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)
total_solute_hbonds() (pytraj.hbond_analysis.DatasetHBond method), [1]
Trajectory (class in pytraj)
(class in pytraj.trajectory)
TrajectoryIterator (class in pytraj)
(class in pytraj.trajectory_iterator)
transform() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.trajectory.Trajectory method)
translate() (in module pytraj), [1]
(in module pytraj.all_actions)
(pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
truncated_name (pytraj.core.c_core.NameType attribute)
type (pytraj.Atom attribute)
(pytraj.topology.SimplifiedAtom attribute)

U

ucellx() (in module pytraj.vector), [1]
ucelly() (in module pytraj.vector), [1]
ucellz() (in module pytraj.vector), [1]
unitcells (pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)

V

values (pytraj.hbond_analysis.DatasetHBond attribute), [1]
vector() (in module pytraj.all_actions)
vector_mask() (in module pytraj.vector), [1]
velocity (pytraj.Frame attribute)
(pytraj.frame.Frame attribute)
velocityautocorr() (in module pytraj)
(in module pytraj.all_actions)
view() (pytraj.Trajectory method)
(pytraj.TrajectoryIterator method)
(pytraj.trajectory.Trajectory method)
(pytraj.trajectory_iterator.TrajectoryIterator method)
volmap() (in module pytraj)
(in module pytraj.all_actions)
volume() (in module pytraj), [1]
(in module pytraj.all_actions)

W

watershell() (in module pytraj), [1]
(in module pytraj.all_actions)
wavelet() (in module pytraj)
(in module pytraj.all_actions)
write_parm() (in module pytraj)
(in module pytraj.io)
write_traj() (in module pytraj), [1]
(in module pytraj.io)
writeparm() (pytraj.topology.ParmFile method)

X

xcorr() (in module pytraj), [1]
(in module pytraj.all_actions)
xyz (pytraj.Frame attribute)
(pytraj.Trajectory attribute)
(pytraj.TrajectoryIterator attribute)
(pytraj.frame.Frame attribute)
(pytraj.trajectory.Trajectory attribute)
(pytraj.trajectory_iterator.TrajectoryIterator attribute)